Microbial ecology often makes assumptions about the relationship between phylogeny and function, but these assumptions can be invalidated by lateral gene transfer. We need to take a broader view of relationships between genes and genomes in order to make better sense out of microbes.

1. http://commons.wikimedia.org/wiki/File:Bison_herd_at_Genesee_Park-2012_03_10_0601.jpg

2. Microbial communities
http://upload.wikimedia.org/wikipedia/commons/2/2d/Bacteria_%28251_31%29_Airborne_microbes.jpg

4. Profiling the microbiome
Marker genes
(e.g., 16S rRNA gene)
Metagenomics:
Functions predicted via similarity to known genes
Marker-gene survey:
Identify best matching relative from a database
nifA
ppk
spo
vanR

5. www.jisponline.com
Supragingival plaque
Subgingival plaque
Patterns in microbial ecology
Species 1: 23%
Species 1: 38%

6. Subgingival Supragingival

7. Jessie
Ning
Characteristic groups
??

8. Pairwise dissimilarity (beta-diversity)
1
2
D1,2

9. What to do with a distance matrix
Hierarchical clustering Ordination (e.g. PCA, PCoA)
Parks and Beiko,
MBE (2012)

10. Arumugam et al. (2011) Nature
“Enterotypes”*

11. Oral sample data from the Human Microbiome Project
Ning and Beiko (in preparation)

12. Oral sample data from the Human Microbiome Project
Ning and Beiko (in preparation)

13. Lawley et al., PLoS Pathog (2012)

14. Wu et al., Nature (2009)

15. Phylogenetic approaches to diversity
UniFrac (Lozupone and Knight, 2007)
Similar Communities Maximally Different Communities
UniFrac Distance Measure = (------) / (------ + ------)
D1,2 = ?

16. There’s more than
one way to do it
Parks and Beiko, ISME J (2013)
*

17. But…
There is a critical assumption in phylogenetic beta diversity:
Microbial FUNCTION and ECOLOGY are intertwined with PHYLOGENY
Is this true?

18. Dagan et al. (2008) PNAS
Maybe
not.

19. Apologies to Brock, 7th ed.

20. Example:
Mycobacterium abscessus – Segniliparus rotundus
Unexpectedly similar!
Smith et al. (2012) PLoS ONE
TetR transcriptional
regulators
Also:
non-ribosomal peptide synthetases
oligopeptide transporters
MmpL / MmpS membrane proteins
Silvia Smith

21. LGT patterns for Clostridium
Whidden et al., 2014 Chris Whidden

22. Smillie et al. (2011) Science
LGT by habitat type
~5% of all compared
genes?

23. Butyrate production – a crucial
function, subject to LGT
Different candidate “species” trees -
All REJECTED!!
Meehan and Beiko (2014) GBE

24. LGT matters in the microbiome!
“…not only the bacterial taxa, but also their
plasmids, are defined by the ecological niche.”
PNAS,2013
PNAS,2012
“…pathogen-driven inflammatory responses in the gut can generate transient enterobacterial
blooms in which conjugative transfer occurs at unprecedented rates.”
PLoSBiol,2007
“…lateral gene transfer, mobile elements, and gene amplification have played important roles in
affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their
environment, and harvest nutrient resources present in the distal intestine.”

25. The point.
•Microbial ecology (whether community
comparisons or something more explicit) can
benefit from understanding the relatedness of
taxonomic groups
•But PHYLOGENY may not capture the whole story
•If we want to better exploit this relatedness, the
best approach may be to explore different ways in
which genomes and also genes may interact

26. LachnoZilla
http://en.wikipedia.org/wiki/File:Godzilla_%2754_design.jpg
From ecology of organisms
To ecology of genes
And maybe, just maybe,
back again

27. Photo courtesy of Dr.Emma Allen Vercoe, University of Guelph
Lachnospiraceae bacterium 3-1-57FAA-CT1

28. Lachno
PATRIC taxonomy
(http://patricbrc.vbi.vt.edu)

29. Meehan and Beiko (2014) Genome Biol Evol

30. 0 1000 2000 3000 4000 5000 6000 7000 8000
Number of Protein-Coding Genes
Sizes of Assembly and Draft Genomes of Class Clostridia
Zilla

31. What makes
LachnoZilla
LachnoZilla ?

32. C. difficile
C. bolteae
….
“Virulence-associated protein”
Recombinase / resolvase
Conjugation proteins
Transposases, transposases,
transposases
Extremely good matches to
other genomes
(> 95% ID, > 95% coverage)

33. LZ & friends:
Clostridium sp. KLE 1755
Clostridiales bacterium VE202-29
Clostridiales bacterium VE202-27
C. hathewayi
C. bolteae
C. clostridioforme
Eubacterium
*
*
*
*
*
*
*
* 279 genomes
Brutal / no taxonomy
Conserved marker-gene tree

34. Close relative
Distant relative
Another distant relative
Genome-centric graphs
Edge weights are proportional to shared genes
Other people who have done this kind of thing: Gipsi Lima-Mendes, Eric Bapteste, Tal Dagan

35. P. aeruginosa
P. fluorescens
P. lePewtida
P. syringae
P. entomophila
P. stutzeri
P. mendocina
Catherine Holloway
“Plume”
Holloway and Beiko, 2010

36. LachnoZilla (and friends)
best-hit graph
!

37. Close relative
(expected)

38. Distant relative
(not so expected)

39. Selective sharing

40. Gene-centric graphs
Edge weights are proportional to similarity of distribution
LZ
Genome
1
Genome
2
Genome
3
Genome
4
Genome
5
Genome
6
Gene 1     × ×
Gene 2     × 
Gene 3    × × 
Gene 4 × × ×   
Gene 2
Gene 3
Gene 1
Gene 4

41. Legionaminic acid
Acetylneuraminic acid
(pathogen associated)
Bacteroides pectinophilus
Butyrivibrio proteoclasticus
Eubacterium plexicaudatum
Roseburia
Neighbors
Weirdly named isolates

42. Mystery isolate #1
(made-up example)

43. Mystery isolate #2
(made-up example)

44. Genome ecology
• Adapts existing techniques developed for deer and
microbial populations
• Can identify modules that may be shared and reused,
and overlay other information:
• Microbial community structure
• Phylogenetic trees
• Construction is agnostic to microbial habitat and role,
and to putative gene functions
• Since we don’t know a lot of this (hypothetical protein /
Lachnospiraceae protein blah blah blah)
• It may not work very well (techniques fail or teach us
nothing new)

45. So…
• There are connections between distant relatives that almost certainly
play a role in pathogenesis and other ecological roles
• Our ability to understand these systems is limited for several reasons:
• Most microorganisms are not understood or even described at all
• Many genes lack reliable functional predictions
• So…many…genes…
• So…much…diversity…
• An ecology of genomes may help us establish linkages and shared
properties of genes and microorganisms, which we might then map
up to the microbial community

46. Thanks!
Microbial ecology
• Donovan Parks
• Jessie Ning
LachnoZilla
• Emma Allen-Vercoe
• Ben Wright
• Eyre Nomi
LGT stories
• Catherine Holloway
• Rob Eveleigh, John Archibald
• Silvia Smith, Darren Martin
• Conor Meehan
• Chris Whidden, Norbert Zeh
• Beiko, Blouinlabs
• CGEB people
FEMS Microbiology Reviews, 2013
Funding: NSERC, CIHR, Killam Trusts, CGEB, CFI, NSHRF, Computer Science

47. Fin
FIN